Mailman 3 March 2016 - yt-dev

Issue #1182: OverflowError with annotate_domain() or annotate_axes() (yt_analysis/yt)
by Michael Zingale 06 Mar '16

06 Mar '16

New issue 1182: OverflowError with annotate_domain() or annotate_axes() https://bitbucket.org/yt_analysis/yt/issues/1182/overflowerror-with-annotat… Michael Zingale: Using this script with the test dataset `maestro_subCh_plt00248` results in ``` File "yt/utilities/lib/misc_utilities.pyx", line 343, in yt.utilities.lib.misc_utilities.zlines (yt/utilities/lib/misc_utilities.c:7768) OverflowError: value too large to convert to int ``` when either `annotate_domain()` or `annotate_axes()` is used (they are commented out in the script. ``` #!/usr/bin/env python import matplotlib matplotlib.use('agg') import sys import yt import numpy as np from yt.visualization.volume_rendering.api import \ Scene, \ Camera, \ VolumeSource # this is for the wdconvect problem def doit(plotfile): ds = yt.load(plotfile) ds.periodicity = (True, True, True) cm = "coolwarm" field = ('boxlib', 'radial_velocity') ds._get_field_info(field).take_log = False sc = Scene() # add a volume: select a sphere center = (0, 0, 0) R = (5.e8, 'cm') dd = ds.sphere(center, R) vol = VolumeSource(dd, field=field) sc.add_source(vol) # transfer function vals = [-5.e6, -2.5e6, -1.25e6, 1.25e6, 2.5e6, 5.e6] sigma = 3.e5 tf = yt.ColorTransferFunction((min(vals), max(vals))) tf.clear() cm = "coolwarm" for v in vals: tf.sample_colormap(v, sigma**2, colormap=cm) #, alpha=0.2) sc.get_source(0).transfer_function = tf cam = Camera(ds, lens_type="perspective") cam.resolution = (1280, 720) cam.position = 1.5*ds.arr(np.array([5.e8, 5.e8, 5.e8]), 'cm') # look toward the center -- we are dealing with an octant center = ds.domain_left_edge normal = (center - cam.position) normal /= np.sqrt(normal.dot(normal)) cam.switch_orientation(normal_vector=normal, north_vector=[0., 0., 1.]) cam.set_width(ds.domain_width) sc.camera = cam #sc.annotate_axes() #sc.annotate_domain(ds) sc.render() sc.save("subchandra_test.png", sigma_clip=6.0) sc.save_annotated("subchandra_test_annotated.png", text_annotate=[[(0.05, 0.05), "t = {}".format(ds.current_time.d), dict(horizontalalignment="left")], [(0.5,0.95), "Maestro simulation of He convection on a white dwarf", dict(color="y", fontsize="24", horizontalalignment="center")]]) if __name__ == "__main__": # Choose a field plotfile = "" try: plotfile = sys.argv[1] except: sys.exit("ERROR: no plotfile specified") doit(plotfile) ```

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Issue #1181: Opaque object does not get rescaled when length-width ratios of camera and image are different (yt_analysis/yt)
by Suoqing Ji 04 Mar '16

04 Mar '16

New issue 1181: Opaque object does not get rescaled when length-width ratios of camera and image are different https://bitbucket.org/yt_analysis/yt/issues/1181/opaque-object-does-not-get… Suoqing Ji: Here is an example of plane-parallel lens. ![plane-parallel.png](https://bitbucket.org/repo/BXbAb/images/4133714937-plane-parallel.png)

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A change to the new volume rendering API
by Nathan Goldbaum 03 Mar '16

03 Mar '16

Hi all, Right now I'm trying to resolve the issues the new VR interface has when you try to specify a volume rendering scene using data that has units attached. Right now, the scene and camera object don't have any knowledge about the units of the data being rendered. At the same time, there are places where the camera, lens and scene assume things like the "width" and "position" *do* have units, which can break in annoying ways. Unfortunately, the way the VR infrastructure is set up right now, it's very difficult for the scene, RenderSource, camera, and lens to all have a consistent unit system. \ I *could* just attach a unit registry to the scene object, but then since all of these different objects get created independently, it doesn't help to have a unit system defined as part of the scene object, since I can't access the scene from the camera object. What I'd like to do to fix this is to alter the VR API. Instead of being able to do something like: sc = Scene() cam = Camera() sc.camera = cam I'd like to make it so you need to do: sc = Scene() sc.add_camera() This way I can ensure that the camera object always has a reference to the Scene object it's attached to, and thus I'll always be able to refer to a consistent unit system. Does anyone have any objections to this? -Nathan

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Issue #1180: PhasePlot and negative numbers (yt_analysis/yt)
by Alex Hill 03 Mar '16

03 Mar '16

New issue 1180: PhasePlot and negative numbers https://bitbucket.org/yt_analysis/yt/issues/1180/phaseplot-and-negative-num… Alex Hill: yt.PhasePlot drops cells with negative velocities because it is initialized with the axis as a log: ``` #!python f = yt.PhasePlot(box, 'temperature', 'velocity_z',['cell_mass'], weight_field=None,fractional=True) f.set_log('velocity_z', False) f.show() ``` In this code, every cell with velocity_z < 0 is blank. This can be fixed by calling set_ylim() after set_log(): ``` #!python f = yt.PhasePlot(box, 'temperature', 'velocity_z',['cell_mass'], weight_field=None,fractional=True) f.set_log('velocity_z', False) ax = f.plots['cell_mass'].axes ax.set_ylim(-5e7,5e7) f.show() ``` but automatic determination of the axis limits does not work. It would be good to invalidate the plot limits after calling set_log() to determine the axis limits automatically.

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Issue #1179: Loading particle files in Flash with DatasetSeries (yt_analysis/yt)
by Alex Hill 03 Mar '16

03 Mar '16

New issue 1179: Loading particle files in Flash with DatasetSeries https://bitbucket.org/yt_analysis/yt/issues/1179/loading-particle-files-in-… Alex Hill: I would like to see an analog of the particle_filename option in yt.load in yt.DatasetSeries for Flash (and possibly other) datasets in which the particle data is stored in a separate file from the main data. If loading a single file, I can do ``` #!python d = yt.load("file_hdf5_plt_cnt_0100", particle_filename="file_hdf5_part_0100") ``` I’d like to do something like ``` #!python ts = yt.DatasetSeries("file_hdf5_plt_cnt_0*0", particle_filename="file_hdf5_part_0*0") ```

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Issue #1178: Error when plotting filtered particle data with derived fields (yt_analysis/yt)
by Anonymous 03 Mar '16

03 Mar '16

New issue 1178: Error when plotting filtered particle data with derived fields https://bitbucket.org/yt_analysis/yt/issues/1178/error-when-plotting-filter… Anonymous:

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Issue #1177: Requirements should be installed automatically when installing via pip (yt_analysis/yt)
by Thomas Edwards 03 Mar '16

03 Mar '16

New issue 1177: Requirements should be installed automatically when installing via pip https://bitbucket.org/yt_analysis/yt/issues/1177/requirements-should-be-ins… Thomas Edwards: When installing a python package with `pip`, I would expect it to install the necessary packages for it to work. For `yt` I have to manually install the other requirements such as `h5py`. The list of requirements is shown on the frontpage but some do not match the names of the packages that `pip` recognise. For example, how do I install `libpng`?

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Issue #1176: Activating yt is non-trivial when installing via pip (yt_analysis/yt)
by Anonymous 03 Mar '16

03 Mar '16

New issue 1176: Activating yt is non-trivial when installing via pip https://bitbucket.org/yt_analysis/yt/issues/1176/activating-yt-is-non-trivi… Anonymous: On the yt-project.org front page, it says that you can simply install yt using `pip install yt`. However, I could not figure out how to activate it, since I could not find the installation directory (I still haven't found it yet). It would be nice if the `pip install yt` method automatically activated yt

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Open Astronomy has been accepted for GSOC 2016
by DVD PS 03 Mar '16

03 Mar '16

Hello everyone!!! Great tnews!! and I cannot type for teh excitment I have in me!!! This year open astronomy is being the umbrella for all these projects (and maybe more that want to form part) for the Google Summer of Code. https://summerofcode.withgoogle.com/organizations/?sp-search=open%20astrono… Thanks to all the admins for the different organisations that helped with the proposal, the website, mailing lists and of course, the mentors for providing ideas. Yuuuuuhuuuuuuuuuuuuuuuuuuuuuuu!!!! David

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POLL: A New Default Colormap
by Matthew Turk 01 Mar '16

01 Mar '16

Hi folks, The current default colormap that yt uses is called "Algae," and it's been with us for a while. Recently some of us on the yt-dev mailing list (which is open to join!) have begun to look at alternate colormaps that have better characteristics, particularly from an accessibility perspective. If you have the time, it would be really, *really* helpful if you could take this anonymous, two question (only one of which is mandatory!) poll about which of the four candidates we've come up with you like the best. http://goo.gl/forms/D4qQqkPIMq Thanks very much! The poll will be open at least a week, and I'll report back the results here sometime after that. -Matt

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